At stake are issues of realism in the set (glass looks realer and what's more, actors won't accidentally put their hands through it... which looks unreal) plus adding a little variety in gloss (a whole world as flat paint gets dull) versus the possibility that glass will reflect lights and create a problem. Glare can be a BIG problem. As an example, look at this photo of a very cool glass stage - see that white reflection?
Photo of glass stage borrowed from Made-in-China.com Cool, huh?
The solution I'm proposing right now - 'cause the builder needs to build right now - is that we use the plexi, but make it easily removable.